Bayesian nonparametric models for peak identification in MALDI-TOF mass spectroscopy

We present a novel nonparametric Bayesian approach based on L\'{e}vy Adaptive Regression Kernels (LARK) to model spectral data arising from MALDI-TOF (Matrix Assisted Laser Desorption Ionization Time-of-Flight) mass spectrometry. This model-based approach provides identification and quantification of proteins through model parameters that are directly interpretable as the number of proteins, mass and abundance of proteins and peak resolution, while having the ability to adapt to unknown smoothness as in wavelet based methods. Informative prior distributions on resolution are key to distinguishing true peaks from background noise and resolving broad peaks into individual peaks for multiple protein species. Posterior distributions are obtained using a reversible jump Markov chain Monte Carlo algorithm and provide inference about the number of peaks (proteins), their masses and abundance. We show through simulation studies that the procedure has desirable true-positive and false-discovery rates. Finally, we illustrate the method on five example spectra: a blank spectrum, a spectrum with only the matrix of a low-molecular-weight substance used to embed target proteins, a spectrum with known proteins, and a single spectrum and average of ten spectra from an individual lung cancer patient.Comment: Published in at http://dx.doi.org/10.1214/10-AOAS450 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

A Neural Network for Synthesizing the Pitch of an Acoustic Source

This article describes a neural network model capable of generating a spatial representation of the pitch of an acoustic source. Pitch is one of several auditory percepts used by humans to separate multiple sound sources in the environment from each other. The model provides a neural instantiation of a type of "harmonic sieve". It is capable of quantitatively simulating a large body of psychoacoustical data, including new data on octave shift perception.Air Force Office of Scientific Research (90-0128, 90-0175); Defense Advanced Research Projects Agency (90-0083); National Science Foundation (IRI 90-24877); American Society for Engineering Educatio

Detecting Extrasolar Planets with Integral Field Spectroscopy

Observations of extrasolar planets using Integral Field Spectroscopy (IFS), if coupled with an extreme Adaptive Optics system and analyzed with a Simultaneous Differential Imaging technique (SDI), are a powerful tool to detect and characterize extrasolar planets directly; they enhance the signal of the planet and, at the same time, reduces the impact of stellar light and consequently important noise sources like speckles. In order to verify the efficiency of such a technique, we developed a simulation code able to test the capabilities of this IFS-SDI technique for different kinds of planets and telescopes, modelling the atmospheric and instrumental noise sources. The first results obtained by the simulations show that many significant extrasolar planet detections are indeed possible using the present 8m-class telescopes within a few hours of exposure time. The procedure adopted to simulate IFS observations is presented here in detail, explaining in particular how we obtain estimates of the speckle noise, Adaptive Optics corrections, specific instrumental features, and how we test the efficiency of the SDI technique to increase the signal-to-noise ratio of the planet detection. The most important results achieved by simulations of various objects, from 1 M_J to brown dwarfs of 30 M_J, for observations with an 8 meter telescope, are then presented and discussed.Comment: 60 pages, 37 figures, accepted in PASP, 4 Tables adde

Nanoparticle-doped electrospun fiber random lasers with spatially extended light modes

Complex assemblies of light-emitting polymer nanofibers with molecular materials exhibiting optical gain can lead to important advance to amorphous photonics and to random laser science and devices. In disordered mats of nanofibers, multiple scattering and waveguiding might interplay to determine localization or spreading of optical modes as well as correlation effects. Here we study electrospun fibers embedding a lasing fluorene-carbazole-fluorene molecule and doped with titania nanoparticles, which exhibit random lasing with sub-nm spectral width and threshold of about 9 mJ cm^-2 for the absorbed excitation fluence. We focus on the spatial and spectral behavior of optical modes in the disordered and non-woven networks, finding evidence for the presence of modes with very large spatial extent, up to the 100 micrometer-scale. These findings suggest emission coupling into integrated nanofiber transmission channels as effective mechanism for enhancing spectral selectivity in random lasers and correlations of light modes in the complex and disordered material.Comment: 22 pages, 6 figure

Understanding hydrogen recombination line observations with ALMA and EVLA

Hydrogen recombination lines are one of the major diagnostics of H II region physical properties and kinematics. In the near future, the Expanded Very Large Array (EVLA) and the Atacama Large Millimeter Array (ALMA) will allow observers to study recombination lines in the radio and sub-mm regime in unprecedented detail. In this paper, we study the properties of recombination lines, in particular at ALMA wavelengths. We find that such lines will lie in almost every wideband ALMA setup and that the line emission will be equally detectable in all bands. Furthermore, we present our implementation of hydrogen recombination lines in the adaptive-mesh radiative transfer code RADMC-3D. We particularly emphasize the importance of non-LTE (local thermodynamical equilibrium) modeling since non-LTE effects can drastically affect the line shapes and produce asymmetric line profiles from radially symmetric H II regions. We demonstrate how these non-LTE effects can be used as a probe of systematic motions (infall & outflow) in the gas. We use RADMC-3D to produce synthetic observations of model H II regions and study the necessary conditions for observing such asymmetric line profiles with ALMA and EVLA.Comment: MNRAS in pres